title: ExonSuite: algorithmically optimizing alternative gene splicing for the PUF proteins.
abstract: The stability of mRNA and its translation is a vital process necessary for proper protein production. The specificity of the regulation is controlled by specific RNA motifs and regulatory proteins. Pumilio/fem-3 mRNA-binding factor (PUF) proteins are usually used in regulating mRNA stability as well as translation. Here, we optimized a PUF protein target finder program to understand the natural diversity of RNA recognition by this family of proteins. ExonSuite is available to compile and run at https://github.com/dilanustek/ExonSuite.
authors.affiliation: Grinnell College, Computer Science Department, USA. ustekdil@grinnell.edu
authors.forename: Dilan
authors.initials: D
authors.lastname: Ustek
authors.forename: Abraham
authors.initials: A
authors.lastname: Kohrman
authors.forename: Bogdan
authors.initials: B
authors.lastname: Krstic
authors.forename: Karissa
authors.initials: K
authors.lastname: Fernandez
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D001665:Binding Sites; D002144:Callithrix; D019295:Computational Biology / Q000379:methods*; D020224:Expressed Sequence Tags; D051379:Mice; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012984:Software; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D014422:Turkeys
chemical_list: D016601:RNA-Binding Proteins; D014157:Transcription Factors